-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_9455809-9594594

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_7073-T1
Valid prediction for snap_scaffold_3-snap.1870-T1
Valid prediction for snap_scaffold_3-snap.1875-T1
Valid prediction for snap_scaffold_3-snap.1890-T1
Valid prediction for snap_scaffold_3-snap.1873-T1
Valid prediction for snap_scaffold_3-snap.1879-T1
Valid prediction for snap_scaffold_3-snap.1865-T1
Valid prediction for HiQ_model.g4612.t1
Valid prediction for snap_scaffold_3-snap.1884-T1
Valid prediction for snap_scaffold_3-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_7077-T1
Valid prediction for snap_scaffold_3-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_7084-T1
Valid prediction for pasa_asmbl_40227.p1
Valid prediction for GlimmerHMM_glimmerT_7061-T1
Valid prediction for GlimmerHMM_glimmerT_7067-T1
Valid prediction for GlimmerHMM_glimmerT_7069-T1
Valid prediction for GlimmerHMM_glimmerT_7082-T1
Valid prediction for GlimmerHMM_glimmerT_7063-T1
Valid prediction for snap_scaffold_3-snap.1864-T1
Valid prediction for snap_scaffold_3-snap.1886-T1
Valid prediction for CodingQuarry_transcript_46236-T1
Valid prediction for Augustus_model.g4617.t1
Valid prediction for GlimmerHMM_glimmerT_7081-T1
Valid prediction for snap_scaffold_3-snap.1860-T1
Valid prediction for snap_scaffold_3-snap.1862-T1
Valid prediction for snap_scaffold_3-snap.1887-T1
Valid prediction for snap_scaffold_3-snap.1871-T1
Valid prediction for snap_scaffold_3-snap.1869-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for Augustus_model.g4609.t1
Valid prediction for GlimmerHMM_glimmerT_7086-T1
Valid prediction for GlimmerHMM_glimmerT_7075-T1
Valid prediction for Augustus_model.g4619.t1
Valid prediction for GlimmerHMM_glimmerT_7085-T1
Valid prediction for snap_scaffold_3-snap.1889-T1
Valid prediction for GlimmerHMM_glimmerT_7078-T1
Valid prediction for Augustus_model.g4615.t1
Valid prediction for GlimmerHMM_glimmerT_7060-T1
Valid prediction for GlimmerHMM_glimmerT_7079-T1
Valid prediction for GlimmerHMM_glimmerT_7066-T1
Valid prediction for GlimmerHMM_glimmerT_7071-T1
Valid prediction for GlimmerHMM_glimmerT_7087-T1
Couldn't classify 61365, 61671
Couldn't classify 61996, 62048
Sorry, prediction pasa_asmbl_39054.p2 fails validation.
(ACC)	 AG	61365-61671	GT	AGG
(ACG)	 AG	61996-62048	CC	CCC
-recovered pasa_asmbl_39054.p2, internal, 61365, 61671
Valid prediction for GlimmerHMM_glimmerT_7074-T1
Valid prediction for GlimmerHMM_glimmerT_7064-T1
Valid prediction for Augustus_model.g4608.t1
Valid prediction for GlimmerHMM_glimmerT_7076-T1
Valid prediction for snap_scaffold_3-snap.1883-T1
Couldn't classify 7183, 7332
Couldn't classify 8858, 9038
Sorry, prediction pasa_asmbl_39057.p1 fails validation.
(CCC)	 CT	7183-7332	GT	AGG
(GGA)	 AG	7674-7841	GT	AGG
(AGC)	 AG	8021-8142	GT	AGG
(CAG)	 AG	8858-9038	GT	AGG
-recovered pasa_asmbl_39057.p1, internal, 7674, 7841
-recovered pasa_asmbl_39057.p1, internal, 8021, 8142
-recovered pasa_asmbl_39057.p1, internal, 8858, 9038
Valid prediction for GlimmerHMM_glimmerT_7072-T1
Valid prediction for Augustus_model.g4614.t1
Valid prediction for GlimmerHMM_glimmerT_7083-T1
Valid prediction for snap_scaffold_3-snap.1885-T1
Valid prediction for snap_scaffold_3-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_7062-T1
Couldn't classify 2988, 4043
Sorry, prediction pasa_asmbl_39058.p1 fails validation.
(ATG)	 GA	2988-4043	TT	CAT
Valid prediction for snap_scaffold_3-snap.1866-T1
Valid prediction for Augustus_model.g4618.t1
Valid prediction for snap_scaffold_3-snap.1882-T1
Couldn't classify 10227, 10290
Sorry, prediction pasa_asmbl_39055.p1 fails validation.
(CCA)	 GC	10227-10290	GT	AGG
(ACA)	 AG	10586-10735	GT	CAG
(GTT)	 AG	12045-12197	GT	AGG
(ATG)	 AG	12279-12388	GT	AGG
(GGG)	 AG	12694-12815	GT	AGG
(CTG)	 AG	12916-13000	GT	AGG
(GTA)	 AG	13110-13222	GT	AGG
(GTC)	 AG	13518-13665	GT	TGG
(CCG)	 AG	14339-14584	GG	GAG
add_exon() Sorry, pasa_asmbl_39055.p1 12279-12388-initial-1 is invalid.
-recovered pasa_asmbl_39055.p1, initial, 12279, 12388
-recovered pasa_asmbl_39055.p1, terminal, 14339, 14584
-recovered pasa_asmbl_39055.p1, internal, 10586, 10735
-recovered pasa_asmbl_39055.p1, internal, 12045, 12197
-recovered pasa_asmbl_39055.p1, internal, 12279, 12388
-recovered pasa_asmbl_39055.p1, internal, 12694, 12815
-recovered pasa_asmbl_39055.p1, internal, 12916, 13000
-recovered pasa_asmbl_39055.p1, internal, 13110, 13222
-recovered pasa_asmbl_39055.p1, internal, 13518, 13665
Valid prediction for Augustus_model.g4616.t1
Valid prediction for snap_scaffold_3-snap.1874-T1
Valid prediction for GlimmerHMM_glimmerT_7070-T1
Valid prediction for snap_scaffold_3-snap.1872-T1
Valid prediction for snap_scaffold_3-snap.1868-T1
Valid prediction for Augustus_model.g4611.t1
Valid prediction for Augustus_model.g4613.t1
Valid prediction for snap_scaffold_3-snap.1888-T1
Valid prediction for snap_scaffold_3-snap.1878-T1
Valid prediction for snap_scaffold_3-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_7065-T1
Valid prediction for GlimmerHMM_glimmerT_7080-T1
Valid prediction for Augustus_model.g4610.t1
Valid prediction for snap_scaffold_3-snap.1861-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7068-T1
Valid prediction for snap_scaffold_3-snap.1891-T1
Valid prediction for snap_scaffold_3-snap.1876-T1
Valid prediction for snap_scaffold_3-snap.1863-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11292, rend_intergenic: 9176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20107, rend_intergenic: 16455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25785, rend_intergenic: 22211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36126, rend_intergenic: 31075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40633, rend_intergenic: 36461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45649, rend_intergenic: 41468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88496, rend_intergenic: 85811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89484, rend_intergenic: 89125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99097, rend_intergenic: 90857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100465, rend_intergenic: 100413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118424, rend_intergenic: 106884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 32515, rend_intergenic: 32512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138786
-exon list size: 317


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 11292, rend_intergenic: 9176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20107, rend_intergenic: 16455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25785, rend_intergenic: 22211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36126, rend_intergenic: 31075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40633, rend_intergenic: 36461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45649, rend_intergenic: 41468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88496, rend_intergenic: 85811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89484, rend_intergenic: 89125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99097, rend_intergenic: 90857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100465, rend_intergenic: 100413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118424, rend_intergenic: 106884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 32515, rend_intergenic: 32512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support